Why Deployment Isn’t Always Easy

Rolling out Microsoft Intune can feel like trying to change the tires on a moving car. On paper, the benefits are obvious: one platform to manage devices, enforce policies, and secure data.

But when it comes time to actually deploy, reality sets in: devices don’t always enroll smoothly, apps misbehave, and your IT team ends up chasing down strange sync errors at 2 a.m.

The good news? These bumps in the road are normal, and they’re solvable. Let’s break down the 10 most common challenges we see during Intune deployments and, more importantly, how to overcome them without losing your sanity.

Challenge 1: Sync & Connectivity Issues

It always starts innocently: a device refuses to show up in the right group, or a user swears they can’t access email even though they’re “in Intune.” Nine times out of ten, the culprit is a sync timing mismatch between Intune and Azure AD.

💡 Our tip: Don’t panic. Use user group filtering to avoid those weird mismatches, and run Microsoft’s Network Connectivity test to pinpoint where the connection is breaking down.

Challenge 2: Device Enrollment Failures

You’ve planned your rollout, shipped devices, and…some just won’t enroll. Maybe they retire halfway through, maybe apps don’t uninstall cleanly.

💡 Our take: This is where bulk enrollment profiles and a solid test group save the day. Re-enrollment usually clears up stubborn cases, but if it doesn’t, don’t be shy about escalating with Microsoft support. (We’ve all

been there.)

Challenge 3: Application Deployment Roadblocks

For the most part, Intune is smooth when deploying apps. But custom, in-house apps? They’re the wildcard. If they aren’t packaged correctly, you’ll hit errors.

💡 Pro move: Always repackage and pilot test before you unleash apps on the entire organization. The Win32 app packaging tool is your friend here. Think of it as the dress rehearsal before opening night.

Challenge 4: Policy Misconfiguration

Intune policies are powerful — but also unforgiving. If a compliance policy is even slightly off, users can find themselves locked out of resources. Cue the help desk flood.

💡 Best practice: Roll out new policies in phases. Start small, verify compliance, and only then scale up. Think of it like flipping switches gradually, not slamming the main breaker.

Challenge 5: Data Security Gaps

One of the worst scenarios: a device fails to set up its container, leaving corporate data sitting unprotected on someone’s personal phone.

💡 Golden rule: If the container isn’t working, wipe and re-enable. Don’t try to duct-tape it. And lean on MAM (Mobile Application Management) to enforce protection at the app level, so even personal devices stay safe without invading privacy.

Challenge 6: OS Compatibility

Here’s a classic: half your fleet is running the latest OS, the other half is clinging to versions that belong in a museum.Intune won’t always play nice with outdated systems.

💡 Lesson learned: Do an OS readiness audit before rollout. Publish requirements early and plan for upgrades or replacements. It’s easier to have that conversation with leadership up front than explain why enrollment failed later.

Challenge 7: Console Complexity

The Intune console is powerful, but let’s be honest: it can feel like navigating an IKEA warehouse. Every new feature adds another menu, and suddenly, your admins are lost in the maze.

💡 Our suggestion: Use role-based access control (RBAC) to keep teams focused only on what they need. And if it still feels overwhelming, don’t hesitate to bring in experts. (Hypershift’s team lives in this console daily — we know the shortcuts.)

Challenge 8: AD Integration & Authentication Failures

It’s always the little things. Something as simple as a username format can stop authentication cold. If users don’t log in as <username>@<domain>, Intune won’t recognize them.

💡 Quick win: Double-check your Azure AD Connect settings and federation. Sometimes the fix really is that simple.

Challenge 9: MFA & Continuous Authentication Issues

Multi-factor authentication is essential, but it can also frustrate users. SMS codes fail, biometrics misfire, and suddenly productivity takes a hit. Worse, some MFA methods aren’t as secure as they should be.

💡 Pro tip: Push toward phishing-resistant MFA methods like FIDO2 keys or Microsoft Authenticator. They’re not only safer, but they cut down on support tickets from annoyed users.

Challenge 10: Monitoring & Compliance Fatigue

Here’s the hard truth: deployment is just the beginning. Without ongoing monitoring, even the best setup will drift out of compliance. Policies get outdated, devices slip through the cracks, and visibility erodes.

💡 What works: Invest in continuous monitoring. Tools like Policy Reporting v3 give real-time feedback, but someone still has to act on it.

Keys to Success

The difference between a painful rollout and a successful one comes down to planning and follow-through.

• Define what success looks like (cost savings, fewer tools, stronger compliance).
• Balance security with user experience so employees don’t feel punished.
• Treat deployment as a long-term strategy, not a one-and-done project.

Why It’s Worth It

When you push through these challenges, Intune pays off:

• One solution for both MDM and MAM
• Support for both BYOD and corporate-owned
• devices
• Full separation of personal and corporate data
• Remote wipe, retire, and re-enroll at your fingertips
• Inventory and asset control in one place
• Compliance with frameworks like GDPR, HIPAA, and PCI-DSS

That’s not just IT efficiency, it’s organizational resilience. And you don’t have to tackle deployment alone, our team can help you plan the rollout, configure policies, and support implementation so you get to value faster.

How Hypershift Can Help

Here’s the thing: you don’t have to tackle all of this alone. At Hypershift, we’ve helped hundreds of organizations — from banks to healthcare providers — roll out Intune without the headaches.

We handle the heavy lifting:

• Designing and testing policies
• Integrating Intune with SCCM and Microsoft 365
• Monitoring compliance 24x7
• Offering everything from air cover support to full managed services

So whether you need an extra set of hands during rollout or a long-term partner to keep Intune running smoothly, we’ve got you covered.

Stuck on one of these Intune roadblocks?

‍Whether it’s enrollment failures, app deployment errors, policy lockouts, or MFA frustration, Hypershift can diagnose the root cause and stabilize your environment fast.

Click the button below to get deployment support from our Intune specialists.